Enable 'lite' version of QC analysis and mutations without a `tree.json` file

[sidneymbell]

For many pathogens, it would be super useful to be able to do at least a 'lite' version of QC analysis and mutation calling with just the reference sequence / i.e., without requiring a tree.json file.

Context being that this would cut the time required to prep a new pathogen-specific reference dataset by probably 75%+ (making the tree also implies having to gather and clean a representative dataset, infer and iterate on clade_membership assignments, advanced understanding of how to use augur, etc.)

[corneliusroemer]

This may be quite easy to do, either by having a template for a dummy tree with just a single tip=root, or by modifying Nextclade to set up such a dummy tree.

[corneliusroemer]

Dummy tree implementation is trivial, I just made one. Here is one anyone can use, needs no modification whatsoever for it to work :)

Just remove the .txt which is necessary for Github to allow it to be uploaded.

tree.json.txt

[sidneymbell]

Ahhh beautiful, thank you!!

[ivan-aksamentov]

Cleaning up old issues.

This is now possible since Nextclade v3 - it does not require a tree to run.